# This file lists ddGs for mutations to Bacillus subtilis cold shock protein b (CspB-B).  The
# exception to this is that I have excluded ddG values for mutations to active site residues or
# residues that are known to be crucially involved in function.  The reason is that these mutations
# may be thermodynamically stabilizing, but selected against by functional pressures.  The
# ddG values are for free energies of folding, so a positive ddG value indicates a destabilizing
# mutation.  All ddG values given below are in units of kcal/mol.  Each ddG value is preceded by 
# the reference from with it was taken. 
# 
# [1] AV Gribenko and GI Makhatadze. "Role of the charge-charge interactions in defining
#      stability and halophilicity of the CspB proteins." J Mol Biol, 366:842-856 (2007)
#      This paper looks at charge-charge interactions in cold shock protein with the idea
#      of determing how these interactions contribute to both the stability of the folded
#      and unfolded state.  There is a strong dependence of stability on ionic strength.
#      They seem to conclude that there is not a large contribution of the charge-charge
#      interactions in the denatured conformations, although I'm not entirely sure
#      how this conclusion is reached.  Table 1 gives the ddG values for mutations to
#      CspB in kJ/mol for unfolding.  I have taken the value for the unstarred mutants
#      where they are available, otherwise I have taken them for the starred mutants.
#      I have then converted these values to be for folding and in kcal/mol.  For
#      mutations with ddG < -15, I have converted the values to be 15 kJ/mol.  The
#      conversion from kJ/mol to kcal/mol was made using 1 kJ/mol = 0.24 kcal/mol.
E3R	-2.3
E3Q	-1.3
K5E	3.1
K5Q	2.0
K7E	3.6
K7Q	3.6
N10D	-0.3
N10K	1.5
E12K	0.6
K13E	0.3
K13Q	0.1
E19K	0.6
E19Q	0.2
V20Q	1.8
V20E	3.6
V20K	1.9
E21K	0.1
E21Q	0.3
D24K	0.5
D24N	0.7
D25K	1.4
D25Q    0.8
K39E	0.3
K39Q	0.0
E42K	-0.0
E42Q	0.1
E43K	-0.2
E43Q	-0.0
S48K	-0.7
S48E	-0.1
E50K	0.6
E50Q	1.2
E53K	0.2
E53Q	-0.2
N55K	0.1
N55D	-0.5
R56Q	-0.4
K65E	1.7
K65Q	0.8
#
# [2] M Jacob, G Holtermann, D Perl, J Reinstein, T Schindler, MA Geeves, and FX Schmid.
#      "Microsecond folding of the cold shock protein measured by a pressure-jump technique."
#      Biochemistry, 38:2882-2891 (1999).
#      This paper looks at the stability and folding/unfolding of cold shock protein B (CspB).
#      Table 1 gives the ddG values in kJ/mol; I have converted to kcal/mol by multiplying
#      by 0.24.
F27A    0.9
F17A    1.5
F15A    2.1
#
# [3] M Wunderlich, A Martin, and FX Schmid. "Stabilization of the cold shock protein CspB
#      from Bacillus subtilis by evolutionary optimization of coulombic interactions."
#      J Mol Biol, 347:1063-1076 (2005)
#      This paper uses directed evolution to find some mutations to charged residues that
#      stabilize cold shock protein B.  The ddG values are listed in Table 2 (and again
#      in Table 4) in kJ/mol for unfolding.  I have convered to kcal/mol by multiplying
#      by 0.24.
M1R	-1.8
E3K	-2.8
K65I	-1.5
E66K	-2.2
E43S	-0.3
A46K	-1.4
S48K	-1.4
S48R	-1.6
#
# [4] MM Garcia-Mira, D Boehringer, and FX Schmid. "The folding transition state of the cold
#      shock protein is strongly polarized." J Mol Biol, 339:555-569 (2004).
#      This paper looks at mutations that affect the stability and folding of cold shock
#      protein, performing phi-value analysis.  The ddG values are calculated by both
#      thermal and urea denaturation.  Here I have taken the urea values given in Table 3
#      in kJ/mol, I have converted to kcal/mol by multiplying by 0.24.  For the mutations V6T,
#      F15A, and D25A, there are no urea denaturation values, so I have instead taken the thermal
#      ones from Table 1.  Note that all of these mutations (except for the E3L reversion)
#      are on the thermostable L3E background.
L2A	0.4
E3L	-1.3
K5A	2.0
K7A	1.1
N10A	1.7
E12A	0.7
K13A	-0.3
F17A	0.8
I18V	1.2
E19A	-0.3
V26T	1.3
A32G	-0.3
I33A	2.0
L41A	2.7
Q45A	0.6
F49A	3.8
F49L	1.0
I51A	2.1
A60G	2.1
V63A	2.9
V6T	1.3
F15A	1.8
D25A	1.2
#
# [5] D Perl, U Mueller, U Heinemann, and FX Schmid. "Two exposed amino acid residues confer
#      thermostability on a cold shock protein." Nature Structural Biology, 7:380-383 (2000).
#      This paper looks at two mutations that convert mesophilic Bacillus subtilis cold
#      shock protein to have the stability of its thermophilic counterpart.  The ddG values
#      are given in Table 1 for Bs-CspB in kJ/mol; I have converted them to kcal/mol.
E3R	-2.7
E66L	-2.1
#
# [6] A Martin, I Kather, and FX Schmid. "Origins of the high stability of an in vitro
#      selected cold-shock protein." J Mol Biol, 318:1341-1349 (2002).
#      This paper selects a stabilized cold shock protein B (CspB) primarily through
#      surface mutations.  The ddG values are given in Table 1 in kJ/mol; I have converted
#      them to be for kcal/mol.  I have taken the values NOT at high ionic strength.
A46L	-0.8
E3V	-1.8
E66V	-1.7
T64R	-1.1
L2R	0.4
